IMPG1 (interphotoreceptor matrix proteoglycan 1)

Gene

• Entrez ID: 3617
• Gene name: Interphotoreceptor matrix proteoglycan 1
• Gene symbol: IMPG1
• Synonyms (NCBI Gene): GP147, IPM150, RP91, SPACR, VMD4
• Chromosome: 6
• Chromosome location: 6q14.1
• Summary: This gene encodes a protein that is a major component of the retinal interphotoreceptor matrix. The encoded protein is a proteoglycan that is thought to play a role in maintaining viability of photoreceptor cells and in adhesion of the neural retina to th

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs144437882	G>A,T	Likely-pathogenic	Coding sequence variant, missense variant
rs200651043	G>A,C	Likely-pathogenic	Coding sequence variant, stop gained, intron variant, missense variant
rs367576664	G>A	Pathogenic	Coding sequence variant, stop gained
rs373792616	C>T	Likely-pathogenic	Coding sequence variant, stop gained
rs713993045	A>C	Pathogenic	Missense variant, coding sequence variant
rs713993046	C>A	Pathogenic	Splice donor variant
rs713993047	A>G	Pathogenic	Missense variant, coding sequence variant
rs1433546528	C>A	Likely-pathogenic	Splice donor variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT028838	hsa-miR-26b-5p	Microarray	19088304
MIRT722394	hsa-miR-617	HITS-CLIP	19536157
MIRT722392	hsa-miR-5581-3p	HITS-CLIP	19536157
MIRT722393	hsa-miR-670-3p	HITS-CLIP	19536157
MIRT569378	hsa-miR-378j	PAR-CLIP	20371350
MIRT569377	hsa-miR-6839-5p	PAR-CLIP	20371350
MIRT569376	hsa-miR-1180-5p	PAR-CLIP	20371350
MIRT569375	hsa-miR-7114-3p	PAR-CLIP	20371350
MIRT569374	hsa-miR-3167	PAR-CLIP	20371350
MIRT569373	hsa-miR-876-5p	PAR-CLIP	20371350
MIRT569372	hsa-miR-1290	PAR-CLIP	20371350
MIRT569371	hsa-miR-4782-5p	PAR-CLIP	20371350
MIRT569370	hsa-miR-5706	PAR-CLIP	20371350
MIRT569369	hsa-miR-1231	PAR-CLIP	20371350
MIRT569368	hsa-miR-6733-3p	PAR-CLIP	20371350
MIRT722394	hsa-miR-617	HITS-CLIP	19536157
MIRT722392	hsa-miR-5581-3p	HITS-CLIP	19536157
MIRT722393	hsa-miR-670-3p	HITS-CLIP	19536157
MIRT569378	hsa-miR-378j	PAR-CLIP	20371350
MIRT569377	hsa-miR-6839-5p	PAR-CLIP	20371350
MIRT569376	hsa-miR-1180-5p	PAR-CLIP	20371350
MIRT569375	hsa-miR-7114-3p	PAR-CLIP	20371350
MIRT569374	hsa-miR-3167	PAR-CLIP	20371350
MIRT569373	hsa-miR-876-5p	PAR-CLIP	20371350
MIRT569372	hsa-miR-1290	PAR-CLIP	20371350
MIRT569371	hsa-miR-4782-5p	PAR-CLIP	20371350
MIRT569370	hsa-miR-5706	PAR-CLIP	20371350
MIRT569369	hsa-miR-1231	PAR-CLIP	20371350
MIRT569368	hsa-miR-6733-3p	PAR-CLIP	20371350
MIRT1066032	hsa-miR-1253	CLIP-seq
MIRT1066033	hsa-miR-580	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001750	Component	Photoreceptor outer segment	IEA
GO:0001917	Component	Photoreceptor inner segment	IEA
GO:0005201	Function	Extracellular matrix structural constituent	TAS	9691169
GO:0005540	Function	Hyaluronic acid binding	IEA
GO:0005540	Function	Hyaluronic acid binding	ISS
GO:0005576	Component	Extracellular region	IEA
GO:0007601	Process	Visual perception	IEA
GO:0007601	Process	Visual perception	TAS	9691169
GO:0008201	Function	Heparin binding	IEA
GO:0008201	Function	Heparin binding	ISS
GO:0030198	Process	Extracellular matrix organization	IEA
GO:0031012	Component	Extracellular matrix	TAS	9691169
GO:0033165	Component	Interphotoreceptor matrix	IEA
GO:0035374	Function	Chondroitin sulfate binding	ISS
GO:0042995	Component	Cell projection	IEA
GO:0071944	Component	Cell periphery	IEA

Other IDs

• MIM: 602870
• HGNC: 6055
• e!Ensembl: ENSG00000112706

Protein

• UniProt ID: Q17R60
• Protein name: Interphotoreceptor matrix proteoglycan 1 (Interphotoreceptor matrix proteoglycan of 150 kDa) (IPM-150) (Sialoprotein associated with cones and rods)
• Protein function: Chondroitin sulfate-, heparin- and hyaluronan-binding protein (By similarity). May serve to form a basic macromolecular scaffold comprising the insoluble interphotoreceptor matrix (PubMed:9813076). {ECO:0000250|UniProtKB:Q8JIR8, ECO:0000269|PubM
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01390	SEA	234 → 324	SEA domain	Family
  PF01390	SEA	573 → 673	SEA domain	Family

• Tissue specificity: TISSUE SPECIFICITY: Expressed in the retina (at protein level) (PubMed:10601738, PubMed:29777959). In the retina, specifically expressed by cone and rod photoreceptor cells (PubMed:9813076). Localizes to cone and rod photoreceptor cells surrounding the in
• Sequence:

  MYLETRRAIFVFWIFLQVQGTKDISINIYHSETKDIDNPPRNETTESTEKMYKMSTMRRI
  FDLAKHRTKRSAFFPTGVKVCPQESMKQILDSLQAYYRLRVCQEAVWEAYRIFLDRIPDT
  GEYQDWVSICQQETFCLFDIGKNFSNSQEHLDLLQQRIKQRSFPDRKDEISAEKTLGEPG
  ETIVISTDVANVSLGPFPLTPDDTLLNEILDNTLNDTKMPTTERETEFAVLEEQRVELSV
  SLVNQKFKAELADSQSPYYQELAGKSQLQMQKIFKKLPGFKKIHVLGFRPKKEKDGSSST
  EMQLTAIFKRHSAEAKSPASDLLSFDSNKIESEEVYHGTMEEDKQPEIYLTATDLKRLIS
  KALEEEQSLDVGTIQFTDEIAGSLPAFGPDTQSELPTSFAVITEDATLSPELPPVEPQLE
  TVDGAEHGLPDTSWSPPAMASTSLSEAPPFFMASSIFSLTDQGTTDTMATDQTMLVPGLT
  IPTSDYSAISQLALGISHPPASSDDSRSSAGGEDMVRHLDEMDLSDTPAPSEVPELSEYV
  SVPDHFLEDTTPVSALQYITTSSMTIAPKGRELVVFFSLRVANMAFSNDLFNKSSLEYRA
  LEQQFTQLLVPYLRSNLTGFKQLEILNFRNGSVIVNSKMKFAKSVPYNLTKAVHGVLEDF
  RSAAAQQLHLEIDSYSLNIEPADQADPCKFLACGEFAQCVKNERTEEAECRCKPGYDSQG
  SLDGLEPGLCGPGTKECEVLQGKGAPCRLPDHSENQAYKTSVKKFQNQQNNKVISKRNSE
  LLTVEYEEFNHQDWEGN

• Sequence length: 797

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Benign concentric annular macular dystrophy	Likely pathogenic; Pathogenic	rs770887047, rs775770292	RCV001637979 RCV005363271	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
IMPG1-related disorder	Pathogenic	rs367576664	RCV004755779	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Isolated macular dystrophy	Likely pathogenic; Pathogenic	rs373792616	RCV001199479	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinal dystrophy	Pathogenic; Likely pathogenic	rs2149482319, rs770887047, rs2481526979, rs373792616, rs986664547	RCV004815582 RCV003891108 RCV003891118 RCV004817781 RCV001074720	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Retinitis pigmentosa	Likely pathogenic; Pathogenic	rs770887047, rs1433546528	RCV003324567 RCV001199480	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Vitelliform macular dystrophy 2	Pathogenic	rs713993046	RCV001199481	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Vitelliform macular dystrophy 4	Pathogenic; Likely pathogenic	rs2149482319, rs770887047, rs1783079545, rs2535897794, rs713993045, rs713993046, rs367576664, rs775770292	RCV001637977 RCV001637980 RCV001637981 RCV002466292 RCV000149547 RCV000149548 RCV000149549 RCV005363271	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ADULT-ONSET FOVEOMACULAR VITELLIFORM DYSTROPHY	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONE-ROD DYSTROPHIES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lymphoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Macular dystrophy	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
MACULAR DYSTROPHY, CONCENTRIC ANNULAR	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MACULAR DYSTROPHY, VITELLIFORM, 4	—	Disgenet, HPO Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 91	—	Disgenet, HPO Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveal melanoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
VITELLIFORM MACULAR DYSTROPHY	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Vitelliform macular dystrophy 1	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Vitelliform macular dystrophy 5	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adult-onset foveomacular vitelliform dystrophy	Foveomacular Vitelliform Dystrophy	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Adult-Onset Vitelliform Macular Dystrophy	Vitelliform Macular Dystrophy	ORPHANET_DG	23993198		★☆☆☆☆ Found in Text Mining only
Adult-Onset Vitelliform Macular Dystrophy	Vitelliform Macular Dystrophy	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Age related macular degeneration	Age-related macular degeneration	BEFREE	23993198, 9719369		★☆☆☆☆ Found in Text Mining only
Age related macular degeneration	Age-related macular degeneration	HPO_DG			★☆☆☆☆ Found in Text Mining only
Chorioretinal atrophy progressive bifocal	Chorioretinal atrophy	Pubtator	9719369	Associate	★☆☆☆☆ Found in Text Mining only
Choroideremia	Choroideremia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Drusen	Drusen	BEFREE	17760704		★☆☆☆☆ Found in Text Mining only
Drusen	Drusen	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypertension	Hypertension	Pubtator	19421330	Associate	★☆☆☆☆ Found in Text Mining only
Juvenile-Onset Vitelliform Macular Dystrophy	Vitelliform Macular Dystrophy	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Leber Congenital Amaurosis	Leber Congenital Amaurosis	BEFREE	11726612		★☆☆☆☆ Found in Text Mining only
Macular Degeneration	Macular degeneration	Pubtator	23993198	Associate	★☆☆☆☆ Found in Text Mining only
Macular dystrophy	Macular dystrophy	BEFREE	23993198, 9719369		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Macular dystrophy	Macular dystrophy	CLINVAR_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Macular dystrophy retinal 1 North Carolina type	Macular dystrophy	Pubtator	9719369	Associate	★☆☆☆☆ Found in Text Mining only
MACULAR DYSTROPHY, VITELLIFORM, 4	Macular dystrophy, vitelliform	UNIPROT_DG	23993198		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MACULAR DYSTROPHY, VITELLIFORM, 4	Macular dystrophy, vitelliform	GENOMICS_ENGLAND_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MACULAR DYSTROPHY, VITELLIFORM, 4	Macular dystrophy, vitelliform	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
North Carolina macular dystrophy	North Carolina Macular Dystrophy	BEFREE	9719369		★☆☆☆☆ Found in Text Mining only
Retinal Diseases	Retinal Diseases	BEFREE	11726612		★☆☆☆☆ Found in Text Mining only
Retinal nonattachment	Retinal nonattachment	HPO_DG			★☆☆☆☆ Found in Text Mining only
Stargardt Disease	Stargardt disease	Pubtator	9719369	Associate	★☆☆☆☆ Found in Text Mining only
Stargardt disease 3	Stargardt Disease	BEFREE	9719369		★☆☆☆☆ Found in Text Mining only
Stargardt disease 3	Stargardt disease	Pubtator	9719369	Associate	★☆☆☆☆ Found in Text Mining only
Vitelliform Macular Dystrophy	Vitelliform Macular Dystrophy	BEFREE	23993198, 24702842, 25085631		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Vitelliform Macular Dystrophy	Vitelliform macular dystrophy	Pubtator	23993198, 35900727	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Vitelliform Macular Dystrophy	Vitelliform Macular Dystrophy	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations